import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
-import com.stevesoft.pat.Regex;
-
/**
* Base class for Ensembl REST service clients
*
* @see https://github.com/Ensembl/ensembl-rest/wiki/Change-log
* @see http://rest.ensembl.org/info/rest?content-type=application/json
*/
- private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "5.0";
+ private static final String LATEST_ENSEMBLGENOMES_REST_VERSION = "6.3";
- private static final String LATEST_ENSEMBL_REST_VERSION = "5.0";
+ private static final String LATEST_ENSEMBL_REST_VERSION = "6.3";
private static final String REST_CHANGE_LOG = "https://github.com/Ensembl/ensembl-rest/wiki/Change-log";
- private static Map<String, EnsemblInfo> domainData;
-
- // @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
- private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
+ private static Map<String, EnsemblData> domainData;
private final static long AVAILABILITY_RETEST_INTERVAL = 10000L; // 10 seconds
private final static long VERSION_RETEST_INTERVAL = 1000L * 3600; // 1 hr
- private static final Regex PROTEIN_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)P[0-9]{11}$");
-
- private static final Regex TRANSCRIPT_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)T[0-9]{11}$");
-
- private static final Regex GENE_REGEX = new Regex(
- "(ENS)([A-Z]{3}|)G[0-9]{11}$");
+ protected static final String CONTENT_TYPE_JSON = "?content-type=application/json";
static
{
- domainData = new HashMap<String, EnsemblInfo>();
- domainData.put(ENSEMBL_REST,
- new EnsemblInfo(ENSEMBL_REST, LATEST_ENSEMBL_REST_VERSION));
- domainData.put(ENSEMBL_GENOMES_REST, new EnsemblInfo(
- ENSEMBL_GENOMES_REST, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ domainData = new HashMap<>();
+ domainData.put(DEFAULT_ENSEMBL_BASEURL,
+ new EnsemblData(DEFAULT_ENSEMBL_BASEURL, LATEST_ENSEMBL_REST_VERSION));
+ domainData.put(DEFAULT_ENSEMBL_GENOMES_BASEURL, new EnsemblData(
+ DEFAULT_ENSEMBL_GENOMES_BASEURL, LATEST_ENSEMBLGENOMES_REST_VERSION));
}
protected volatile boolean inProgress = false;
*/
public EnsemblRestClient()
{
- this(ENSEMBL_REST);
+ super();
+
+ /*
+ * initialise domain info lazily
+ */
+ if (!domainData.containsKey(ensemblDomain))
+ {
+ domainData.put(ensemblDomain,
+ new EnsemblData(ensemblDomain, LATEST_ENSEMBL_REST_VERSION));
+ }
+ if (!domainData.containsKey(ensemblGenomesDomain))
+ {
+ domainData.put(ensemblGenomesDomain, new EnsemblData(
+ ensemblGenomesDomain, LATEST_ENSEMBLGENOMES_REST_VERSION));
+ }
}
/**
setDomain(d);
}
- /**
- * Answers true if the query matches the regular expression pattern for an
- * Ensembl transcript stable identifier
- *
- * @param query
- * @return
- */
- public boolean isTranscriptIdentifier(String query)
- {
- return query == null ? false : TRANSCRIPT_REGEX.search(query);
- }
-
- /**
- * Answers true if the query matches the regular expression pattern for an
- * Ensembl protein stable identifier
- *
- * @param query
- * @return
- */
- public boolean isProteinIdentifier(String query)
- {
- return query == null ? false : PROTEIN_REGEX.search(query);
- }
-
- /**
- * Answers true if the query matches the regular expression pattern for an
- * Ensembl gene stable identifier
- *
- * @param query
- * @return
- */
- public boolean isGeneIdentifier(String query)
- {
- return query == null ? false : GENE_REGEX.search(query);
- }
-
@Override
public boolean queryInProgress()
{
boolean checkEnsembl()
{
BufferedReader br = null;
+ String pingUrl = getDomain() + "/info/ping" + CONTENT_TYPE_JSON;
try
{
// note this format works for both ensembl and ensemblgenomes
// info/ping.json works for ensembl only (March 2016)
- URL ping = new URL(
- getDomain() + "/info/ping?content-type=application/json");
+ URL ping = new URL(pingUrl);
/*
* expect {"ping":1} if ok
br = getHttpResponse(ping, null, 2 * 1000);
if (br == null)
{
+ // error reponse status
return false;
}
JSONParser jp = new JSONParser();
} catch (Throwable t)
{
System.err.println(
- "Error connecting to " + PING_URL + ": " + t.getMessage());
+ "Error connecting to " + pingUrl + ": " + t.getMessage());
} finally
{
if (br != null)
}
/**
- * Sends the HTTP request and gets the response as a reader
+ * Sends the HTTP request and gets the response as a reader. Returns null if
+ * the HTTP response code was not 200.
*
* @param url
* @param ids
* in milliseconds
* @return
* @throws IOException
- * if response code was not 200, or other I/O error
*/
protected BufferedReader getHttpResponse(URL url, List<String> ids,
int readTimeout) throws IOException
*/
protected boolean isEnsemblAvailable()
{
- EnsemblInfo info = domainData.get(getDomain());
+ EnsemblData info = domainData.get(getDomain());
long now = System.currentTimeMillis();
*/
private void checkEnsemblRestVersion()
{
- EnsemblInfo info = domainData.get(getDomain());
+ EnsemblData info = domainData.get(getDomain());
JSONParser jp = new JSONParser();
URL url = null;
try
{
- url = new URL(
- getDomain() + "/info/rest?content-type=application/json");
+ url = new URL(getDomain() + "/info/rest" + CONTENT_TYPE_JSON);
BufferedReader br = getHttpResponse(url, null);
+ if (br == null)
+ {
+ return;
+ }
JSONObject val = (JSONObject) jp.parse(br);
String version = val.get("release").toString();
String majorVersion = version.substring(0, version.indexOf("."));
try
{
- url = new URL(
- getDomain() + "/info/data?content-type=application/json");
+ url = new URL(getDomain() + "/info/data" + CONTENT_TYPE_JSON);
br = getHttpResponse(url, null);
if (br != null)
{
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